Molecular Morphology: Deep Phylogeny Using RNA Structures and Related Markers

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We propose a continued re-evaluation of the existing ribosomal RNA data, and other non-coding RNA classes, with secondary-structure-aware methods, focusing on data that will be retrieved by the EST surveys performed by other participating research groups in the DMP. In this context, we will continue to develop and refine algorithms for the derivation of reliable secondary structure models of novel rRNA sequences and other suitable ncRNA classes, as well as develop methods for utilizing the evolution of the secondary structures themselves for reconstructing phylogenies. The autonomous derivation of clade-specific “molecular morphological characters”, such as sequence features, e.g. particularly wellconserved patterns or insertions, from multiple sequence alignments, and phylogenetically informative structural features will be explored. The development and application of a model that accounts for the character evolution of ncRNA secondary structure as a practical structural alignment tool and the consideration of “realistic” mutational events will be of interest. Additionally, nucleotide substitution models that distinguish between conserved and “other” regions, as well as incorporate the slower evolution of the structural elements themselves will be developed. It will be explored whether the structure-based and structure-enhanced phylogenetic methods can be extended to amino acid sequences. Novel and improved software for rRNA based phylogeny will be provided to the research community.